Metazoa-hydrothermal-vent

1 Background

2 Set up in R

library(tidyverse); library(patchwork)

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## ✓ readr   2.0.0     ✓ forcats 0.5.1

## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()

library(gt); library(viridis)

## Loading required package: viridisLite

library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
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2.1 Import exisiting data

merged_tax <- read_delim("../microeuks_deepbiosphere_datamine/microeuk-amplicon-survey/data-input/taxonomy.tsv", delim = "\t")
merged_asv <- read_delim("../microeuks_deepbiosphere_datamine/microeuk-amplicon-survey/data-input/microeuk-merged-asv-table.tsv", delim = "\t", skip = 1)
metadata <- read.delim("../microeuks_deepbiosphere_datamine/microeuk-amplicon-survey/data-input/samplelist-metadata.txt")

asv_wtax <- merged_asv %>%
  select(FeatureID = '#OTU ID', everything()) %>%
  pivot_longer(cols = !FeatureID,
               names_to = "SAMPLE", values_to = "value") %>%
  left_join(merged_tax, by = c("FeatureID" = "Feature ID")) %>%
  left_join(metadata) %>%
  filter(!grepl("Siders_", SAMPLE)) %>% 
  filter(SAMPLETYPE != "Incubation") %>% 
  mutate(DATASET = case_when(
    grepl("_GR_", SAMPLE) ~ "GR",
    grepl("Gorda", SAMPLE) ~ "GR",
    grepl("_MCR_", SAMPLE) ~ "MCR",
    grepl("Axial", SAMPLE) ~ "Axial",
  TRUE ~ "Control or blank")) %>%
    separate(Taxon, c("Domain", "Supergroup",
                  "Phylum", "Class", "Order",
                  "Family", "Genus", "Species"), sep = ";", remove = FALSE) %>% 
  unite(SAMPLENAME, SITE, SAMPLETYPE, YEAR, VENT, SAMPLEID, sep = " ", remove = FALSE)

Save to this directory

save(asv_wtax, metadata, file = "data-input/ASVs-18S-survey-03122021.RData")

3 Broad overview of metazoa

load("data-input/ASVs-18S-survey-03122021.RData", verbose = TRUE)

## Loading objects:
##   asv_wtax
##   metadata

# unique(asv_wtax$Supergroup)
# colnames(asv_wtax)
list_of_metazoa <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta") %>% 
  select(Domain:Species) %>% 
  distinct()
dim(list_of_metazoa)

## [1] 190   8

3.1 Table of all taxa

Output table of all unique metazoan names in dataset.

list_of_metazoa %>% 
  select(-Domain, -Supergroup) %>% 
  arrange(Phylum, Class, Order) %>% 
  gt(
    rowname_col = c("Phylum")
  ) %>% 
  tab_header(title = "Opisthokonta by Phylum")

Opisthokonta by Phylum
	Class	Order	Family	Genus	Species
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_D	Stephanoecidae_Group_D_X	Stephanoecidae_Group_D_X_sp.
Choanoflagellida	Choanoflagellatea	Acanthoecida	NA	NA	NA
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_E	Stephanoecidae_Group_E_X	Stephanoecidae_Group_E_X_sp.
Choanoflagellida	Choanoflagellatea	Acanthoecida	Acanthoecidae_Group_G	Acanthoecidae_Group_G_X	Acanthoecidae_Group_G_X_sp.
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_H	Stephanoecidae_Group_H_X	Stephanoecidae_Group_H_X_sp.
Choanoflagellida	Choanoflagellatea	Acanthoecida	Acanthoecidae_Group_G	NA	NA
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_D	NA	NA
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_H	NA	NA
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_I	Stephanoecidae_Group_I_X	Stephanoecidae_Group_I_X_sp.
Choanoflagellida	Choanoflagellatea	Acanthoecida	Stephanoecidae_Group_I	NA	NA
Choanoflagellida	Choanoflagellatea	Choanoflagellatea_X	Choanoflagellatea_X_Group_L	Choanoflagellatea_X_Group_L_X	Choanoflagellatea_X_Group_L_X_sp.
Choanoflagellida	Choanoflagellatea	Choanoflagellatea_X	Choanoflagellatea_X_Group_P	Choanoflagellatea_X_Group_P_X	Choanoflagellatea_X_Group_P_X_sp.
Choanoflagellida	Choanoflagellatea	Choanoflagellatea_X	Choanoflagellatea_XX	Salpingoeca_XX	Salpingoeca_XX_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	NA	NA	NA
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_O	Monosigidae_Group_O_X	Monosigidae_Group_O_X_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	Salpingoecidae_Group_C2	Salpingoecidae_Group_C2_X	Salpingoecidae_Group_C2_X_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_B	Monosigidae_Group_B_X	Monosigidae_Group_B_X_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	Salpingoecidae_Group_C2	NA	NA
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_A	Monosigidae_Group_A_X	Monosigidae_Group_A_X_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_A	NA	NA
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_A	Monosiga	Monosiga_brevicollis
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_A	Codosiga	Codosiga_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_A	Salpingoeca_A	Salpingoeca_A_sp.
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_M	Salpingoeca_M	Salpingoeca_tuba
Choanoflagellida	Choanoflagellatea	Craspedida	Monosigidae_Group_B	NA	NA
Choanoflagellida	Choanoflagellatea	Craspedida	Salpingoecidae_Group_C1	Salpingoecidae_Group_C1_X	Salpingoecidae_Group_C1_X_sp.
Choanoflagellida	Choanoflagellatea	NA	NA	NA	NA
Choanoflagellida	Choanoflagellida_X	Choanoflagellida_XX	NA	NA	NA
Choanoflagellida	Choanoflagellida_X	Choanoflagellida_XX	Choanoflagellida_XXX	Choanoflagellida_XXXX	Choanoflagellida_XXXX_sp.
Choanoflagellida	Choanoflagellida_X	Choanoflagellida_XX	Choanoflagellida_XX_Clade-2	Choanoflagellida_XX_Clade-2_X	Choanoflagellida_XX_Clade-2_X_sp.
Choanoflagellida	NA	NA	NA	NA	NA
Fungi	Ascomycota	Pezizomycotina	Eurotiomycetes	Eurotiomycetes_X	Eurotiomycetes_X_sp.
Fungi	Ascomycota	Pezizomycotina	Sordariomycetes	Sordariomycetes_X	Sordariomycetes_X_sp.
Fungi	Ascomycota	Pezizomycotina	NA	NA	NA
Fungi	Ascomycota	Pezizomycotina	Pezizomycetes	Pezizomycetes_X	Pezizomycetes_X_sp.
Fungi	Ascomycota	Pezizomycotina	Dothideomycetes	NA	NA
Fungi	Ascomycota	Pezizomycotina	Pezizomycotina_X	Pezizomycotina_XX	Pezizomycotina_XX_sp.
Fungi	Ascomycota	Pezizomycotina	Eurotiomycetes	NA	NA
Fungi	Ascomycota	Pezizomycotina	Dothideomycetes	Verruconis	Verruconis_gallopava
Fungi	Ascomycota	Pezizomycotina	Eurotiomycetes	Aspergillus	NA
Fungi	Ascomycota	Pezizomycotina	Sordariomycetes	NA	NA
Fungi	Ascomycota	Pezizomycotina	Pezizomycotina_X	NA	NA
Fungi	Ascomycota	Pezizomycotina	Sordariomycetes	Ascotricha	NA
Fungi	Ascomycota	Saccharomycotina	Saccharomycetales	NA	NA
Fungi	Ascomycota	Saccharomycotina	Saccharomycetales	Meyerozyma	Meyerozyma_guilliermondii
Fungi	Ascomycota	Saccharomycotina	Saccharomycetales	Saccharomycetales_X	Saccharomycetales_X_sp.
Fungi	Ascomycota	Saccharomycotina	Saccharomycetales	Candida	NA
Fungi	Ascomycota	Saccharomycotina	Saccharomycetales	Saccharomyces	NA
Fungi	Ascomycota	Taphrinomycotina	Taphrinomycetes	Taphrina	NA
Fungi	Ascomycota	Taphrinomycotina	Schizosaccharomycetes	Schizosaccharomyces	Schizosaccharomyces_japonicus
Fungi	Ascomycota	Taphrinomycotina	Taphrinomycetes	NA	NA
Fungi	Ascomycota	Taphrinomycotina	Taphrinomycotina_X	Saitoella	Saitoella_complicata
Fungi	Ascomycota	NA	NA	NA	NA
Fungi	Basidiomycota	Agaricomycotina	Agaricomycetes	Agaricomycetes_X	Agaricomycetes_X_sp.
Fungi	Basidiomycota	Agaricomycotina	Agaricomycetes	Auricularia	Auricularia_auricula-judae
Fungi	Basidiomycota	Agaricomycotina	Agaricomycetes	NA	NA
Fungi	Basidiomycota	Agaricomycotina	Agaricomycetes	Hyphodontia	NA
Fungi	Basidiomycota	Agaricomycotina	Tremellomycetes	Tremellomycetes_X	Tremellomycetes_X_sp.
Fungi	Basidiomycota	Agaricomycotina	Agaricomycetes	Pleurotus	NA
Fungi	Basidiomycota	Agaricomycotina	Tremellomycetes	Trichosporon	NA
Fungi	Basidiomycota	Agaricomycotina	Tremellomycetes	NA	NA
Fungi	Basidiomycota	Agaricomycotina	Agaricomycetes	Trichaptum	NA
Fungi	Basidiomycota	Basidiomycota_X	Basidiomycota_XX	Nephridiophaga	Nephridiophaga_blattellae
Fungi	Basidiomycota	Pucciniomycotina	Agaricostilbomycetes	NA	NA
Fungi	Basidiomycota	Pucciniomycotina	Microbotryomycetes	Microbotryomycetes_X	Microbotryomycetes_X_sp.
Fungi	Basidiomycota	Pucciniomycotina	NA	NA	NA
Fungi	Basidiomycota	Pucciniomycotina	Pucciniomycetes	NA	NA
Fungi	Basidiomycota	Pucciniomycotina	Cystobasidiomycetes	Rhodotorula	NA
Fungi	Basidiomycota	Pucciniomycotina	Cystobasidiomycetes	Rhodotorula	Rhodotorula_mucilaginosa
Fungi	Basidiomycota	Pucciniomycotina	Pucciniomycetes	Septobasidium	NA
Fungi	Basidiomycota	Pucciniomycotina	Cystobasidiomycetes	Cystobasidiomycetes_X	Cystobasidiomycetes_X_sp.
Fungi	Basidiomycota	Pucciniomycotina	Microbotryomycetes	Rhodosporidium	NA
Fungi	Basidiomycota	Pucciniomycotina	Cystobasidiomycetes	Rhodotorula	Rhodotorula_glutinis
Fungi	Basidiomycota	Pucciniomycotina	Cystobasidiomycetes	NA	NA
Fungi	Basidiomycota	Pucciniomycotina	Cystobasidiomycetes	Sporobolomyces	Sporobolomyces_roseus
Fungi	Basidiomycota	Ustilaginomycotina	Exobasidiomycetes	Exobasidiomycetes_X	Exobasidiomycetes_X_sp.
Fungi	Basidiomycota	Ustilaginomycotina	Ustilaginomycetes	NA	NA
Fungi	Basidiomycota	Ustilaginomycotina	Exobasidiomycetes	Malassezia	NA
Fungi	Blastocladiomycota	Blastocladiomycotina	Blastocladiomycetes	NA	NA
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycetes	NA	NA
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycetes	Chytridiomycetes_X	Chytridiomycetes_X_sp.
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycetes	Rhyzophidiales_X	Rhyzophidiales_X_sp.
Fungi	Chytridiomycota	Chytridiomycotina	NA	NA	NA
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycetes	Spizellomyces	Spizellomyces_sp.
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycotina_X	Chytridiomycotina_XX	Chytridiomycotina_XX_sp.
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycetes	Spizellomycetales-and-Rhizophlyctidales	Spizellomycetales-and-Rhizophlyctidales_sp.
Fungi	Chytridiomycota	Chytridiomycotina	Chytridiomycetes	Phlyctochytrium	Phlyctochytrium_planicorne
Fungi	Cryptomycota	Cryptomycotina	Cryptomycotina_X	Cryptomycotina_XX	Cryptomycotina_XX_sp.
Fungi	Fungi_X	Fungi_XX	Fungi_XXX	Fungi_XXXX	Fungi_XXXX_sp.
Fungi	Fungi_X	Fungi_XX	Fungi_XXX	NA	NA
Fungi	Microsporidiomycota	Microsporidiomycotina	Microsporidiomycotina_X	Microsporidium	Microsporidium_sp.
Fungi	Microsporidiomycota	Microsporidiomycotina	Microsporidiomycotina_X	Facilispora	Facilispora_margolisi
Fungi	Mucoromycota	Mucoromycotina	Mucoromycotina_X	Mortierella	Mortierella_wolfii
Fungi	Mucoromycota	Mucoromycotina	Mucoromycotina_X	Mucoromycotina_XX	Mucoromycotina_XX_sp.
Fungi	Mucoromycota	Mucoromycotina	Mucoromycotina_X	NA	NA
Fungi	NA	NA	NA	NA	NA
Mesomycetozoa	Ichthyosporea	Ichthyosphonida	Ichthyophonidae_Amoebidianae	NA	NA
Mesomycetozoa	Ichthyosporea	Ichthyosphonida	NA	NA	NA
Mesomycetozoa	Ichthyosporea	Ichthyosphonida	Pseudoperkinsidae	NA	NA
Mesomycetozoa	Ichthyosporea	Ichthyosphonida	Abeoformidae_Group_MAIP_2	Abeoformidae_Group_MAIP_2_X	Abeoformidae_Group_MAIP_2_X_sp.
Mesomycetozoa	Ichthyosporea	Rhynosporida	NA	NA	NA
Metazoa	Annelida	Annelida_X	Annelida_XX	NA	NA
Metazoa	Annelida	Annelida_X	Annelida_XX	Paralvinella	NA
Metazoa	Annelida	Annelida_X	Siboglinidae	NA	NA
Metazoa	Annelida	Annelida_X	Annelida_XX	Vigtorniella	Vigtorniella_sp.
Metazoa	Annelida	Annelida_X	Annelida_XX	Protodrilus	NA
Metazoa	Arthropoda	Chelicerata	Arachnida	NA	NA
Metazoa	Arthropoda	Chelicerata	Pycnogonida	NA	NA
Metazoa	Arthropoda	Crustacea	Maxillopoda	NA	NA
Metazoa	Arthropoda	Crustacea	Maxillopoda	Maxillopoda_X	Maxillopoda_X_sp.
Metazoa	Arthropoda	Crustacea	Ostracoda	NA	NA
Metazoa	Arthropoda	Crustacea	Maxillopoda	Calocalanus	Calocalanus_sp.
Metazoa	Arthropoda	Crustacea	Malacostraca	NA	NA
Metazoa	Arthropoda	Crustacea	Maxillopoda	Clausocalanus	Clausocalanus_furcatus
Metazoa	Arthropoda	Crustacea	Maxillopoda	Oithona	Oithona_sp.
Metazoa	Arthropoda	Crustacea	Maxillopoda	Metridia	Metridia_sp.
Metazoa	Arthropoda	Crustacea	Maxillopoda	Eudiaptomus	Eudiaptomus_sp.
Metazoa	Arthropoda	Hexapoda	Insecta	NA	NA
Metazoa	Bryozoa	Bryozoa_X	Bryozoa_XX	NA	NA
Metazoa	Chaetognatha	Aphragmophora	Aphragmophora_X	NA	NA
Metazoa	Cnidaria	Cnidaria_X	Hydrozoa	NA	NA
Metazoa	Cnidaria	Cnidaria_X	Scyphozoa	NA	NA
Metazoa	Cnidaria	Cnidaria_X	Hydrozoa	Hydrozoa_X	Hydrozoa_X_sp.
Metazoa	Cnidaria	Cnidaria_X	Hydrozoa	Apolemia	Apolemia_sp.
Metazoa	Cnidaria	Cnidaria_X	Anthozoa	Nematostella	Nematostella_vectensis
Metazoa	Cnidaria	Cnidaria_X	Anthozoa	NA	NA
Metazoa	Cnidaria	Cnidaria_X	Hydrozoa	Zanclea	Zanclea_sp.
Metazoa	Cnidaria	Cnidaria_X	Hydrozoa	Cordagalma	Cordagalma_cordiforme
Metazoa	Cnidaria	Cnidaria_X	Scyphozoa	Atolla	NA
Metazoa	Cnidaria	Cnidaria_X	Hydrozoa	Clytia	NA
Metazoa	Cnidaria	Cnidaria_X	Scyphozoa	Phacellophora	NA
Metazoa	Cnidaria	Cnidaria_X	Scyphozoa	Cyanea	NA
Metazoa	Cnidaria	Cnidaria_X	Scyphozoa	Aurelia	NA
Metazoa	Craniata	Craniata_X	Teleostei	NA	NA
Metazoa	Craniata	Craniata_X	Lepidosauria	Scincus	Scincus_scincus
Metazoa	Craniata	Craniata_X	Mammalia	NA	NA
Metazoa	Craniata	Craniata_X	Teleostei	Auxis	Auxis_rochei
Metazoa	Craniata	Craniata_X	Teleostei	Salmo	Salmo_salar
Metazoa	Craniata	Craniata_X	Mammalia	Homo	Homo_sapiens
Metazoa	Ctenophora	Ctenophora_X	Ctenophora_XX	NA	NA
Metazoa	Ctenophora	Ctenophora_X	Ctenophora_XX	Beroe	NA
Metazoa	Ctenophora	Ctenophora_X	Ctenophora_XX	Ctenophora_XXX	Ctenophora_XXX_sp.
Metazoa	Echinodermata	Echinodermata_X	Echinodermata_XX	NA	NA
Metazoa	Echinodermata	Echinodermata_X	Echinodermata_XX	Xyloplax	Xyloplax_janetae
Metazoa	Gastrotricha	Gastrotricha_X	Gastrotricha_XX	NA	NA
Metazoa	Hemichordata	Hemichordata_X	Hemichordata_XX	NA	NA
Metazoa	Loricifera	Loricifera_X	Loricifera_XX	Pliciloricus	Pliciloricus_sp.
Metazoa	Mesozoa	Mesozoa_X	Orthonectida	Rhopalura	Rhopalura_ophiocomae
Metazoa	Metazoa_X	Metazoa_XX	Metazoa_XXX	Metazoa_XXXX	Metazoa_XXXX_sp.
Metazoa	Mollusca	Bivalvia	NA	NA	NA
Metazoa	Mollusca	Bivalvia	Protobranchia	NA	NA
Metazoa	Mollusca	Bivalvia	Heteroconchia	NA	NA
Metazoa	Mollusca	Bivalvia	Pectinoida	NA	NA
Metazoa	Mollusca	Cephalopoda	Cephalopoda_X	NA	NA
Metazoa	Mollusca	Gastropoda	Vetigastropoda	NA	NA
Metazoa	Mollusca	Gastropoda	Neritopsina	Depressigyra	Depressigyra_sp.
Metazoa	Mollusca	Gastropoda	Heterobranchia	Rissoella_gastropoda	Rissoella_rissoaformis
Metazoa	Mollusca	Gastropoda	Vetigastropoda	Vetigastropoda_X	Vetigastropoda_X_sp.
Metazoa	Mollusca	Gastropoda	Neritopsina	Depressigyra	NA
Metazoa	Mollusca	Gastropoda	Caenogastropoda	NA	NA
Metazoa	Mollusca	NA	NA	NA	NA
Metazoa	Myxozoa	Myxozoa_X	Myxosporea	Kudoa	NA
Metazoa	Myzostomida	Myzostomida_X	Myzostomida_XX	Myzostoma	NA
Metazoa	Nematoda	Chromadorea	Chromadorea_X	NA	NA
Metazoa	Nematoda	Chromadorea	Chromadorea_X	Chromadorea_XX	Chromadorea_XX_sp.
Metazoa	Nematoda	Chromadorea	Chromadorea_X	Leptolaimus	Leptolaimus_sp.
Metazoa	Nematoda	Chromadorea	NA	NA	NA
Metazoa	Nematoda	Enoplea	Enoplea_X	NA	NA
Metazoa	Nemertea	Nemertea_X	Nemertea_XX	NA	NA
Metazoa	Nemertea	Nemertea_X	Nemertea_XX	Nemertea_XXX	Nemertea_XXX_sp.
Metazoa	Platyhelminthes	Turbellaria	Catenulida	NA	NA
Metazoa	Platyhelminthes	Turbellaria	Polycladida	NA	NA
Metazoa	Platyhelminthes	Turbellaria	Acoelomorpha	NA	NA
Metazoa	Platyhelminthes	Turbellaria	Rhabdocoela	NA	NA
Metazoa	Platyhelminthes	Turbellaria	Prolecithophora	Plagiostomum	NA
Metazoa	Platyhelminthes	Turbellaria	Seriata	NA	NA
Metazoa	Platyhelminthes	Turbellaria	Prolecithophora	NA	NA
Metazoa	Platyhelminthes	Turbellaria	Rhabdocoela	Gyratrix	NA
Metazoa	Porifera	Porifera_X	Calcarea	NA	NA
Metazoa	Porifera	Porifera_X	Hexactinellida	NA	NA
Metazoa	Porifera	Porifera_X	Demospongiae	NA	NA
Metazoa	Porifera	Porifera_X	Demospongiae	Geodia	NA
Metazoa	Rotifera	Rotifera_X	Rotifera_XX	NA	NA
Metazoa	Rotifera	Rotifera_X	Rotifera_XX	Rotifera_XXX	Rotifera_XXX_sp.
Metazoa	Urochordata	Urochordata_X	Ascidiacea	NA	NA
Metazoa	Urochordata	Urochordata_X	Appendicularia	Oikopleura	Oikopleura_dioica
Metazoa	Urochordata	Urochordata_X	Ascidiacea	Cyclosalpa	NA
Metazoa	NA	NA	NA	NA	NA
Opisthokonta_X	Opisthokonta_XX	Opisthokonta_XXX	Opisthokonta_XXXX	Opisthokonta_XXXXX	Opisthokonta_XXXXX_sp.
NA	NA	NA	NA	NA	NA

3.2 Stats on sequence data

# Number of ASVs
tmp <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta")
100*(length(unique(tmp$FeatureID))/length(unique(asv_wtax$FeatureID)))

## [1] 8.849113

# Number of sequences
100*(sum(tmp$value)/sum(asv_wtax$value))

## [1] 27.15345

Total number of ASVs across sites is 1587 - totaling to 8.8% of all ASVs recovered and 27% of all sequences.

3.3 Bar plots of metazoa: Phylum & Class

# head(asv_wtax)
metazoa_all_barplot <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ") %>% 
  group_by(SITE, SAMPLETYPE, Phylum) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  # unite(PhylumClass, Phylum, Class, sep = "-") %>% 
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = Phylum)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  coord_flip() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  scale_fill_viridis(discrete = TRUE, option = "turbo") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")

## `summarise()` has grouped output by 'SITE', 'SAMPLETYPE'. You can override using the `.groups` argument.

## Warning: Ignoring unknown parameters: stroke

ggplotly(metazoa_all_barplot)

Observations: At the phylum level, metazoa made up the most number of 18S sequences recovered. This was followed by Choanoflagellates in the background and plume environments, and then by fungi in the vent habitats.

3.3.1 to the class level

# head(asv_wtax)
metazoa_all_barplot_class <- asv_wtax %>% 
  filter(Supergroup == "Opisthokonta") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ") %>% 
  group_by(SITE, SAMPLETYPE, Phylum, Class) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  unite(PhylumClass, Phylum, Class, sep = "-") %>% 
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = PhylumClass)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  coord_flip() +
  scale_fill_viridis(discrete = TRUE, option = "inferno") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")

## `summarise()` has grouped output by 'SITE', 'SAMPLETYPE', 'Phylum'. You can override using the `.groups` argument.

## Warning: Ignoring unknown parameters: stroke

ggplotly(metazoa_all_barplot_class)

Observations: There’s a shift in the community from the background and plume habitats having higher relative abundances of Ctenophora and Cnidaria sequences and Chanoflagellates (especially in the plume!), to the diffuse flow fluid having a higher relativea bundance of Annelida, Mollusca, and Arthropoda. (things that settle?)

3.3.2 closer look at metazoa only

# head(asv_wtax)
metazoa_only_bar <- asv_wtax %>% 
  filter(Phylum == "Metazoa") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ", remove = FALSE) %>% 
  group_by(SAMPLETYPE, SITE, Class) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  # unite(PhylumClass, Phylum, Class, sep = "-") %>% 
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = Class)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  coord_flip() +
  scale_fill_viridis(discrete = TRUE, option = "rocket") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")

## `summarise()` has grouped output by 'SAMPLETYPE', 'SITE'. You can override using the `.groups` argument.

## Warning: Ignoring unknown parameters: stroke

ggplotly(metazoa_only_bar)

# head(asv_wtax)
metazoa_only_Order_bar <- asv_wtax %>% 
  filter(Phylum == "Metazoa") %>%
  filter(Sample_or_Control == "Sample") %>% 
  # unite(SAMPLETYPE_2, SITE, SAMPLETYPE, sep = " ", remove = FALSE) %>% 
  group_by(SAMPLETYPE, SITE, Class, Order) %>% 
  summarise(SUM_CLASS = sum(value)) %>% 
  unite(ClassOrder, Class, Order, sep = "-") %>%
  ggplot(aes(x = SITE, y = SUM_CLASS, fill = ClassOrder)) +
    geom_bar(stat = "identity", position = "fill", color = "white", stroke = 0.1) +
    theme_classic() +
  facet_grid(SAMPLETYPE ~. , space = "free") +
  coord_flip() +
  scale_fill_viridis(discrete = TRUE, option = "rocket") +
  labs(x = "", y= "Sequence relative abundance") +
  theme(legend.position = "bottom")

## `summarise()` has grouped output by 'SAMPLETYPE', 'SITE', 'Class'. You can override using the `.groups` argument.

## Warning: Ignoring unknown parameters: stroke

ggplotly(metazoa_only_Order_bar)

Observations: When we go to the ‘Order’ level for metazoa, we see that many of the taxa names end with **_X**. This means the level is unknown. In the case of the PR2 database, it is still unclear if this means it is because that level is mis-placed, or they didn’t curate the rest of the sequence?

I used V4 primers. We can explore the PR2 database more here: https://pr2database.github.io/pr2database/articles/pr2database.html

# install.packages(devtools)
# devtools::install_github("pr2database/pr2database")

4 Next steps?

• Sort out database issue
• Is this biogeography helpful?
• Closer look at substrates at Gorda Ridge (larger project)
• Paired samples with other amplicons?